Electrochemical impedance spectroscopy (EIS) is a widely used technique for characterizing materials in electrochemical systems. However, directly connecting the obtained quantities to microstructure-level phenomena is challenging. In this work, we performed detailed electrochemical microstructure simulations to investigate the EIS behavior of phase-separating graphite electrodes. We employed the Cahn-Hilliard phase-field equation to model Li transport and phase transitions in the graphite particles. In single-phase graphite particles, the charge-transfer resistance reflected the total active surface areas. In two-phase coexistence graphite particles with phase boundaries present on the particle surfaces, the simulations exhibited an inductive loop on the EIS curve. In core-shell phase-morphology cases, the EIS measurements reflected only the properties of the shells. The resulting EIS curves were indistinguishable from those in the single-phase cases. While Fick's law of diffusion has been mistakenly employed to model Li transport in phase-separating graphite electrodes, our simulations showed that the EIS curves obtained using the Fickian diffusion model were very similar to those obtained using the Cahn-Hilliard phase-field model. This tool provides unprecedentedly detailed simulations to connect the intrinsic material properties, electrochemical processes in the microstructures, and resulting EIS behavior. Figure 1